RYBP_MOUSE
ID RYBP_MOUSE Reviewed; 228 AA.
AC Q8CCI5; B2RRB6; Q9WVK2;
DT 10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=RING1 and YY1-binding protein;
DE AltName: Full=Death effector domain-associated factor;
DE Short=DED-associated factor;
GN Name=Rybp; Synonyms=Dedaf;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Embryonic gonad;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 2-228, AND INTERACTION WITH YAF2; YY1; CBX2;
RP RING1 AND RNF2.
RC STRAIN=C57BL/10;
RX PubMed=10369680; DOI=10.1093/emboj/18.12.3404;
RA Garcia E., Marcos-Gutierrez C., del Mar Lorente M., Moreno J.C., Vidal M.;
RT "RYBP, a new repressor protein that interacts with components of the
RT mammalian Polycomb complex, and with the transcription factor YY1.";
RL EMBO J. 18:3404-3418(1999).
RN [4]
RP DEVELOPMENTAL STAGE.
RX PubMed=14765135; DOI=10.1038/sj.cdd.4401391;
RA Danen-van Oorschot A.A.M.M., Voskamp P., Seelen M.C.M.J.,
RA van Miltenburg M.H.A.M., Bolk M.W., Tait S.W., Boesen-de Cock J.G.R.,
RA Rohn J.L., Borst J., Noteborn M.H.M.;
RT "Human death effector domain-associated factor interacts with the viral
RT apoptosis agonist Apoptin and exerts tumor-preferential cell killing.";
RL Cell Death Differ. 11:564-573(2004).
RN [5]
RP DISRUPTION PHENOTYPE.
RX PubMed=16055728; DOI=10.1128/mcb.25.16.7193-7202.2005;
RA Pirity M.K., Locker J., Schreiber-Agus N.;
RT "Rybp/DEDAF is required for early postimplantation and for central nervous
RT system development.";
RL Mol. Cell. Biol. 25:7193-7202(2005).
RN [6]
RP SUBUNIT, INTERACTION WITH RING1 AND RNF2, SUBCELLULAR LOCATION, MUTAGENESIS
RP OF 31-THR-PHE-32, AND UBIQUITINATION.
RX PubMed=17070805; DOI=10.1016/j.febslet.2006.10.027;
RA Arrigoni R., Alam S.L., Wamstad J.A., Bardwell V.J., Sundquist W.I.,
RA Schreiber-Agus N.;
RT "The Polycomb-associated protein Rybp is a ubiquitin binding protein.";
RL FEBS Lett. 580:6233-6241(2006).
RN [7]
RP INTERACTION WITH IFT57, AND FUNCTION.
RX PubMed=17874297; DOI=10.1007/s10495-007-0131-3;
RA Stanton S.E., Blanck J.K., Locker J., Schreiber-Agus N.;
RT "Rybp interacts with Hippi and enhances Hippi-mediated apoptosis.";
RL Apoptosis 12:2197-2206(2007).
RN [8]
RP INTERACTION WITH RNF2, SUBUNIT, DOMAIN, DNA-BINDING, AND CIRCULAR
RP DICHROISM.
RX PubMed=19170609; DOI=10.1021/bi801933c;
RA Neira J.L., Roman-Trufero M., Contreras L.M., Prieto J., Singh G.,
RA Barrera F.N., Renart M.L., Vidal M.;
RT "The transcriptional repressor RYBP is a natively unfolded protein which
RT folds upon binding to DNA.";
RL Biochemistry 48:1348-1360(2009).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-123; SER-127 AND SER-130, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Kidney, Lung, Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [10]
RP FUNCTION, AND SUBUNIT.
RX PubMed=22325148; DOI=10.1016/j.cell.2011.12.029;
RA Tavares L., Dimitrova E., Oxley D., Webster J., Poot R., Demmers J.,
RA Bezstarosti K., Taylor S., Ura H., Koide H., Wutz A., Vidal M.,
RA Elderkin S., Brockdorff N.;
RT "RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites
RT independently of PRC2 and H3K27me3.";
RL Cell 148:664-678(2012).
RN [11]
RP INTERACTION WITH RNF2, AND TISSUE SPECIFICITY.
RX PubMed=22226355; DOI=10.1016/j.stem.2011.12.006;
RA Morey L., Pascual G., Cozzuto L., Roma G., Wutz A., Benitah S.A.,
RA Di Croce L.;
RT "Nonoverlapping functions of the Polycomb group Cbx family of proteins in
RT embryonic stem cells.";
RL Cell Stem Cell 10:47-62(2012).
RN [12]
RP FUNCTION.
RX PubMed=27748911; DOI=10.3892/ijo.2016.3718;
RA Zhou H., Li J., Zhang Z., Ye R., Shao N., Cheang T., Wang S.;
RT "RING1 and YY1 binding protein suppresses breast cancer growth and
RT metastasis.";
RL Int. J. Oncol. 49:2442-2452(2016).
RN [13]
RP FUNCTION, AND SUBUNIT.
RX PubMed=28596365; DOI=10.1126/science.aal2512;
RA Almeida M., Pintacuda G., Masui O., Koseki Y., Gdula M., Cerase A.,
RA Brown D., Mould A., Innocent C., Nakayama M., Schermelleh L.,
RA Nesterova T.B., Koseki H., Brockdorff N.;
RT "PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome
RT inactivation.";
RL Science 356:1081-1084(2017).
CC -!- FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1-like
CC complex, a complex class required to maintain the transcriptionally
CC repressive state of many genes, including Hox genes, throughout
CC development. PcG PRC1-like complex acts via chromatin remodeling and
CC modification of histones; it mediates monoubiquitination of histone H2A
CC 'Lys-119', rendering chromatin heritably changed in its expressibility
CC (PubMed:22325148, PubMed:28596365). Component of a PRC1-like complex
CC that mediates monoubiquitination of histone H2A 'Lys-119' on the X
CC chromosome and is required for normal silencing of one copy of the X
CC chromosome in XX females (PubMed:28596365). May stimulate
CC ubiquitination of histone H2A 'Lys-119' by recruiting the complex to
CC target sites (PubMed:22325148, PubMed:28596365). Inhibits
CC ubiquitination and subsequent degradation of TP53, and thereby plays a
CC role in regulating transcription of TP53 target genes (By similarity).
CC May also regulate the ubiquitin-mediated proteasomal degradation of
CC other proteins like FANK1 to regulate apoptosis (PubMed:17874297). May
CC be implicated in the regulation of the transcription as a repressor of
CC the transcriptional activity of E4TF1 (By similarity). May bind to DNA
CC (PubMed:19170609). May play a role in the repression of tumor growth
CC and metastasis in breast cancer by down-regulating SRRM3
CC (PubMed:27748911). {ECO:0000250|UniProtKB:Q8N488,
CC ECO:0000269|PubMed:17874297, ECO:0000269|PubMed:19170609,
CC ECO:0000269|PubMed:22325148, ECO:0000269|PubMed:27748911,
CC ECO:0000269|PubMed:28596365}.
CC -!- SUBUNIT: Monomer. Component of repressive BCOR complex containing
CC Polycomb group subcomplex at least composed of BCOR, PCGF1, RING1 and
CC RNF2/RING2 (By similarity). Component of PCR1-like complexes
CC (PubMed:22325148, PubMed:28596365). Interacts with PCGF1. Part of a
CC PCR1-like complex that contains AUTS2, PCGF5, RNF2, CSNK2B AND RYBP.
CC Interacts with RNF2; the interaction is direct (By similarity).
CC Interacts with CBX2, YAF2, RING1 and RNF2 (PubMed:10369680,
CC PubMed:19170609, PubMed:22226355). Interacts with ubiquitin and
CC ubiquitinated proteins (PubMed:17070805). Interacts with ubiquitinated
CC histone H2A (PubMed:17070805). Interacts with apoptin, DEDD, FADD,
CC CASP8, CASP10, YY1 and GABPB1. Together with GABPB1 and YY1, it forms a
CC ternary complex, probably being the bridge factor between these two
CC transcription factors. Interacts with MDM2, and thereby inhibits
CC ubiquitination of TP53. Identified in a ternary complex containing
CC MDM2, TP53 and RYBP. Interacts with FANK1; may prevent the ubiquitin-
CC mediated proteasomal degradation of FANK1 (By similarity). Interacts
CC with IFT57 (PubMed:17874297). {ECO:0000250|UniProtKB:Q8N488,
CC ECO:0000269|PubMed:10369680, ECO:0000269|PubMed:17070805,
CC ECO:0000269|PubMed:17874297, ECO:0000269|PubMed:19170609,
CC ECO:0000269|PubMed:22226355, ECO:0000269|PubMed:22325148,
CC ECO:0000269|PubMed:28596365}.
CC -!- INTERACTION:
CC Q8CCI5; P30658: Cbx2; NbExp=3; IntAct=EBI-929290, EBI-360174;
CC Q8CCI5; O35730: Ring1; NbExp=4; IntAct=EBI-929290, EBI-929310;
CC Q8CCI5; Q9CQJ4: Rnf2; NbExp=8; IntAct=EBI-929290, EBI-927321;
CC Q8CCI5; P25490: YY1; Xeno; NbExp=2; IntAct=EBI-929290, EBI-765538;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17070805}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q8N488}. Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:17070805}. Note=Primarily found in the nucleus.
CC Detected in a punctate pattern likely to represent Polycomb group (PcG)
CC bodies. {ECO:0000269|PubMed:17070805}.
CC -!- TISSUE SPECIFICITY: Expressed in embryonic stem cells.
CC {ECO:0000269|PubMed:22226355}.
CC -!- DEVELOPMENTAL STAGE: At 9.0 dpc, selectively expressed in cells of the
CC developing nervous system and from day E.5 onwards, expressed
CC ubiquitously. {ECO:0000269|PubMed:14765135}.
CC -!- DOMAIN: Intrinsically unstructured in the absence of binding partners.
CC Folds upon binding to DNA or RNF2. {ECO:0000269|PubMed:19170609}.
CC -!- PTM: Monoubiquitinated.
CC -!- DISRUPTION PHENOTYPE: Embryonically lethal. Embryos die at early
CC postimplantation stage. {ECO:0000269|PubMed:16055728}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD42945.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AK033024; BAC28131.1; -; mRNA.
DR EMBL; BC053016; AAH53016.1; -; mRNA.
DR EMBL; BC080287; AAH80287.1; -; mRNA.
DR EMBL; BC138324; AAI38325.1; -; mRNA.
DR EMBL; BC138325; AAI38326.1; -; mRNA.
DR EMBL; AF101779; AAD42945.1; ALT_INIT; mRNA.
DR CCDS; CCDS39579.1; -.
DR RefSeq; NP_062717.2; NM_019743.3.
DR AlphaFoldDB; Q8CCI5; -.
DR SMR; Q8CCI5; -.
DR BioGRID; 207918; 14.
DR IntAct; Q8CCI5; 13.
DR MINT; Q8CCI5; -.
DR STRING; 10090.ENSMUSP00000098677; -.
DR iPTMnet; Q8CCI5; -.
DR PhosphoSitePlus; Q8CCI5; -.
DR EPD; Q8CCI5; -.
DR jPOST; Q8CCI5; -.
DR MaxQB; Q8CCI5; -.
DR PaxDb; Q8CCI5; -.
DR PeptideAtlas; Q8CCI5; -.
DR PRIDE; Q8CCI5; -.
DR ProteomicsDB; 256853; -.
DR Antibodypedia; 7772; 491 antibodies from 37 providers.
DR DNASU; 56353; -.
DR Ensembl; ENSMUST00000101118; ENSMUSP00000098677; ENSMUSG00000072872.
DR GeneID; 56353; -.
DR KEGG; mmu:56353; -.
DR UCSC; uc009dbw.1; mouse.
DR CTD; 23429; -.
DR MGI; MGI:1929059; Rybp.
DR VEuPathDB; HostDB:ENSMUSG00000072872; -.
DR eggNOG; KOG4477; Eukaryota.
DR GeneTree; ENSGT00390000013995; -.
DR HOGENOM; CLU_095374_0_0_1; -.
DR InParanoid; Q8CCI5; -.
DR OMA; SNKNSHI; -.
DR OrthoDB; 1634090at2759; -.
DR PhylomeDB; Q8CCI5; -.
DR TreeFam; TF350501; -.
DR Reactome; R-MMU-8939243; RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known.
DR Reactome; R-MMU-8953750; Transcriptional Regulation by E2F6.
DR BioGRID-ORCS; 56353; 5 hits in 74 CRISPR screens.
DR ChiTaRS; Rybp; mouse.
DR PRO; PR:Q8CCI5; -.
DR Proteomes; UP000000589; Chromosome 6.
DR RNAct; Q8CCI5; protein.
DR Bgee; ENSMUSG00000072872; Expressed in manus and 232 other tissues.
DR Genevisible; Q8CCI5; MM.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005654; C:nucleoplasm; IDA:MGI.
DR GO; GO:0005634; C:nucleus; IDA:MGI.
DR GO; GO:0031519; C:PcG protein complex; ISO:MGI.
DR GO; GO:0003677; F:DNA binding; IDA:MGI.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0003714; F:transcription corepressor activity; IDA:MGI.
DR GO; GO:0006915; P:apoptotic process; IEA:UniProtKB-KW.
DR GO; GO:0035518; P:histone H2A monoubiquitination; ISO:MGI.
DR GO; GO:0032435; P:negative regulation of proteasomal ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:MGI.
DR GO; GO:0043065; P:positive regulation of apoptotic process; ISS:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR InterPro; IPR039958; RYBP/YAF2.
DR InterPro; IPR033774; YAF2_RYBP.
DR InterPro; IPR001876; Znf_RanBP2.
DR InterPro; IPR036443; Znf_RanBP2_sf.
DR PANTHER; PTHR12920; PTHR12920; 1.
DR Pfam; PF17219; YAF2_RYBP; 1.
DR Pfam; PF00641; zf-RanBP; 1.
DR SMART; SM00547; ZnF_RBZ; 1.
DR SUPFAM; SSF90209; SSF90209; 1.
DR PROSITE; PS01358; ZF_RANBP2_1; 1.
DR PROSITE; PS50199; ZF_RANBP2_2; 1.
PE 1: Evidence at protein level;
KW Apoptosis; Cytoplasm; DNA-binding; Isopeptide bond; Metal-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Ubl conjugation; Zinc; Zinc-finger.
FT CHAIN 1..228
FT /note="RING1 and YY1-binding protein"
FT /id="PRO_0000097551"
FT ZN_FING 21..50
FT /note="RanBP2-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00322"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 47..157
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 143..226
FT /note="Interaction with GABPB1 and FANK1"
FT /evidence="ECO:0000250|UniProtKB:Q8N488"
FT REGION 172..228
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..20
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 53..71
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 75..119
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 122..141
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 99
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8N488"
FT MOD_RES 123
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 127
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 130
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 227
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8N488"
FT CROSSLNK 77
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q8N488"
FT MUTAGEN 31..32
FT /note="TF->AA: Loss of ubiquitin binding."
FT /evidence="ECO:0000269|PubMed:17070805"
FT CONFLICT 143
FT /note="T -> S (in Ref. 3; AAD42945)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 228 AA; 24777 MW; 80E4D647244E213D CRC64;
MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT STRKPRINSQ
LVAQQVAQQY ATPPPPKKEK KEKVEKPDKE KPEKDKDISP SVTKKNTNKK TKPKSDILKD
PPSEANSIQS ANATTKTSET NHTSRPRLKN VDRSTAQQLA VTVGNVTVII TDFKEKTRSS
STSSSTVTSS AGSEQQNQSS SGSESTDKGS SRSSTPKGDM SAVNDESF
